The Enterprise crew cautiously pursues Dr. Arik Soong and his superhuman Augments across hostile Klingon space toward a hidden planet where he intends to raise his Augment army. But in defiance of their "father" Soong, Malik devises a heinous plot to use a bioweapon against a Klingon colony planet, undoubtedly leading to interstellar war, to safeguard the Augments from Enterprise and further Starfleet interference. Malik's rash proposal leads to a rift with Soong.

The Syrranites subject Archer to a potentially lethal mind-meld after learning that information about Surak was placed in his head. Meanwhile, Vulcan officials plot the dissidents' destruction.